''Ideonella sakaiensis'' is a

bacterium Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the ...

from the

genus Genus (; : genera ) is a taxonomic rank above species and below family (taxonomy), family as used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In bino ...

'' Ideonella'' and family Comamonadaceae capable of breaking down and consuming the plastic

polyethylene terephthalate Polyethylene terephthalate (or poly(ethylene terephthalate), PET, PETE, or the obsolete PETP or PET-P), is the most common thermoplastic polymer resin of the polyester family and is used in synthetic fibre, fibres for clothing, packaging, conta ...

(PET) using it as both a carbon and energy source. The bacterium was originally isolated from a sediment sample taken outside of a

plastic bottle A plastic bottle is a bottle constructed from high-density or low density plastic. Plastic bottles are typically used to store liquids such as water, soft drinks, motor oil, cooking oil, medicine, shampoo or milk. They range in sizes, from very ...

recycling Recycling is the process of converting waste materials into new materials and objects. This concept often includes the recovery of energy from waste materials. The recyclability of a material depends on its ability to reacquire the propert ...

facility in Sakai City,

Japan Japan is an island country in East Asia. Located in the Pacific Ocean off the northeast coast of the Asia, Asian mainland, it is bordered on the west by the Sea of Japan and extends from the Sea of Okhotsk in the north to the East China Sea ...

Discovery

''Ideonella sakaiensis'' was first identified in 2016 by a team of researchers led by Kohei Oda of Kyoto Institute of Technology and Kenji Miyamoto of Keio University after collecting a sample of PET-contaminated sediment at a plastic bottle recycling facility in Sakai, Japan. The bacteria was first isolated from a consortium of microorganisms in the sediment sample, which included

protozoa Protozoa (: protozoan or protozoon; alternative plural: protozoans) are a polyphyletic group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic debris. Historically ...

and yeast-like cells. The entire microbial community was shown to mineralize 75% of the degraded PET into carbon dioxide once it had been initially degraded and assimilated by ''Ideonella sakaiensis''.

Characterization

Physical attributes

''Ideonella sakaiensis'' is

gram-negative Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists ...

, aerobic, and rod-shaped. Cells are motile and have a single

flagellum A flagellum (; : flagella) (Latin for 'whip' or 'scourge') is a hair-like appendage that protrudes from certain plant and animal sperm cells, from fungal spores ( zoospores), and from a wide range of microorganisms to provide motility. Many pr ...

. Colonies of ''I. sakaiensis'' are colorless, smooth, and circular. Its size varies from 0.6 to 0.8 μm in width and 1.2-1.5 μm in length.

Chemical attributes

''I. sakaiensis'' also tests positive for oxidase and

catalase Catalase is a common enzyme found in nearly all living organisms exposed to oxygen (such as bacteria, plants, and animals) which catalyzes the decomposition of hydrogen peroxide to water and oxygen. It is a very important enzyme in protecting ...

. The bacterium grows at a pH range of 5.5 to 9.0 (optimally at 7 to 7.5) and a temperature of (optimally at ). Ideonella Sakaiensis Eating Plastics

Use of characteristics

This bacterium's gram negativity gives it resistant abilities and genes; this could include antibiotic resistance. The negativity also means that it has a thin cell wall and a high lipid content. The aerobic aspect of this bacterium means that it can grow and thrive only in an environment that contains oxygen. ''Ideonella sakaiensis'' and other aerobic bacteria therefore survive in oxygen-rich soil that is moist and aerated. The flagellum attached to this bacterium are used as motile organelles and are able to rotate and thrust the cell throughout its environment by creating motion. The bacterium was also shown to grow on the surface of polyethylene terephthalate (PET),a type of plastic, adhering with its thin flagellum. This is shown in the image to the right. The flagellum may also secrete PET-degrading enzymes onto the PET surface known as PETases. Through phylogenetic analysis, the species was shown to be a part of the genus '' Ideonella,'' but possessed a significantly different genome than other known species in the genus, including '' Ideonella dechloratans'' and '' Ideonella azotifigens,'' thus justifying its classification as a new species.

Degradation and assimilation of PET

''Ideonella sakaiensis'' adhere to PET surface and use a secreted PET

hydrolase In biochemistry, hydrolases constitute a class of enzymes that commonly function as biochemical catalysts that use water to break a chemical bond: :\ce \quad \xrightarrowtext\quad \ce This typically results in dividing a larger molecule into s ...

, or PETase, to degrade the PET into mono(2-hydroxyethyl)terephthalic acid (MHET), a

heterodimer In biochemistry, a protein dimer is a macromolecular complex or multimer formed by two protein monomers, or single proteins, which are usually non-covalently bound. Many macromolecules, such as proteins or nucleic acids, form dimers. The word ...

composed of terephthalic acid (TPA) and

ethylene glycol Ethylene glycol ( IUPAC name: ethane-1,2-diol) is an organic compound (a vicinal diol) with the formula . It is mainly used for two purposes: as a raw material in the manufacture of polyester fibers and for antifreeze formulations. It is an odo ...

. The PETase also degrades PET into another intermediate known as Bis-(2-hydroxyethyl) terephthalate (BHET), BHET can be converted into MHET after PET hydrolysis. The ''I. sakaiensis'' PETase functions by hydrolyzing the ester bonds present in PET with high specificity. The resulting MHET is then degraded into its two monomeric constituents by a lipid-anchored MHET hydrolase enzyme, or MHETase, on the cell's outer membrane. The overall mechanism of the PET plastic being broken down is exhibited in the image above. The monomeric constituents such as ethylene glycol is then taken up and used by ''I. sakaiensis'' and many other bacteria. The other constituent; terephthalic acid, a more recalcitrant compound, is imported into the ''I. sakaiensis'' cell via the terephthalic acid transporter protein. Once in the cell, the aromatic terephthalic acid molecule is oxidized by terephthalic acid-1,2-dioxygenase and 1,2-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase into a

catechol Catechol ( or ), also known as pyrocatechol or 1,2-dihydroxybenzene, is an organic compound with the molecular formula . It is the ''ortho'' isomer of the three isomeric benzenediols. This colorless compound occurs naturally in trace amounts. It ...

intermediate. The catechol ring is then cleaved by PCA 3,4-dioxygenase before the compound is integrated into other metabolic pathways (e.g.

TCA cycle The citric acid cycle—also known as the Krebs cycle, Szent–Györgyi–Krebs cycle, or TCA cycle (tricarboxylic acid cycle)—is a series of chemical reaction, biochemical reactions that release the energy stored in nutrients through acetyl-Co ...

). As a result, both of the molecules derived from the PET are used by the cell to produce energy and to build necessary biomolecules. Eventually, the assimilated carbon may be mineralized to carbon dioxide and released into the atmosphere.

Impact and applications

The discovery of ''Ideonella sakaiensis'' has potential importance for the degradation of PET plastics. Prior to its discovery, the only known degraders of PET were a small number of bacteria and fungi, including '' Fusarium solani'', and no organisms were definitively known to degrade PET as a primary carbon and energy source. The discovery of ''I. sakaiensis'' spurred discussion about PET biodegradation as a method of

and

bioremediation Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi in mycoremediation, and plants in phytoremediation), living or dead, is employed for removing environmental pollutants from air, wate ...

. The

wild-type The wild type (WT) is the phenotype of the typical form of a species as it occurs in nature. Originally, the wild type was conceptualized as a product of the standard "normal" allele at a locus, in contrast to that produced by a non-standard, " ...

bacterium is able to colonize and break down a thin (0.2 mm thickness) film of low-crystallinity (soft) PET in approximately 6 weeks, and the responsible PETase enzyme was shown to degrade high-crystallinity (hard) PET approximately 30-fold slower (180 weeks or more than 3 years) than low-crystallinity PET. A large amount of manufactured PET is highly crystalline (e.g. plastic bottles), so it is thought that any prospective applications of the ''I. sakaiensis'' PETase enzyme in recycling programs will need to be preceded by genetic optimization of the enzyme. The MHETase enzyme could also be optimized and used in recycling or bioremediation applications in combination with the PETase enzyme. It degrades the MHET produced by the PETase into ethylene glycol and terephthalic acid. Once formed, these two compounds can be further biodegraded into carbon dioxide by ''I. sakaiensis'' or other microbes, or purified and used to manufacture new PET in an industrial recycling plant setting. ''Ideonella sakaiensis'' is being studied for its PET-degrading capabilities in sewage-fed fisheries. Various strains of this bacterium have been shown not to pose any threat to the growth and cultivation of fish. This species of bacterium makes effective use of PET as a source of carbon, and thrives in wastewater and plastic-polluted water ecosystems, showing its promise as a cost-effective anti-pollutant.

Genetic engineering Genetic engineering, also called genetic modification or genetic manipulation, is the modification and manipulation of an organism's genes using technology. It is a set of Genetic engineering techniques, technologies used to change the genet ...

The PET plastic-degrading enzyme of ''Ideonella sakaiensis'' known as; PETase, has been genetically modified and combined with MHETase to break down PET faster, which also degrades PEF (polyethylene furanoate) plastics. This, along with other approaches, may be useful in recycling and upcycling mixed plastics.

Coagulation filtration system

In 2021, fifth graders Julia Stewart and Jacob Park created a coagulation filtration system concept for Toshiba's ExploraVision contest, using ''Ideonella sakaiensis'' in a process that filters, coagulates, flocculates, and sediments water in a more environmentally friendly and efficient way. This project won the 4-6 division of ExploraVision in the United States.

References

External links

Type strain of ''Ideonella sakaiensis'' at Bac''Dive'' - the Bacterial Diversity Metadatabase
{{Taxonbar, from=Q23034816 Comamonadaceae Bacteria described in 2016 Plastivores